8QU5: 39S ribosomal protein L32, mitochondrial

Name: PDB 8QU5: mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
Published: 2024-06-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2. Determined by electron microscopy at 2.42 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 55
Atoms: 89,817
Mol. weight: 1784.44 kDa
Ligands: PNS, MG, ZN
Released: 26 Jun 2024

Explore 8QU5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QU5 contains 387 α-helices and 379 β-strands across 53 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	101-102	2
β-strand	107-109	3	1
β-strand	116-118	3	1
α-helix	124-145	22
β-strand	156-159	4	2
β-strand	173-176	4	2
α-helix	180-182	3

Chain 1: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	4
β-strand	29-35	7	4
β-strand	42-47	6	4
β-strand	52-63	12	4

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-64	8
α-helix	66-71	6
α-helix	73-85	13

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	15
α-helix	121	1
β-strand	122-125	4	15
α-helix	133-135	3
α-helix	138-144	7
β-strand	147-149	3	15
α-helix	152-160	9
β-strand	172	1	16
α-helix	178-180	3

Chain 5: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	48-50	3
β-strand	59	1	33
β-strand	71	1	33
α-helix	72-73	2
α-helix	85-87	3
α-helix	90-92	3
α-helix	103	1
β-strand	104-107	4	34
α-helix	117-124	8
β-strand	126-130	5	35
α-helix	134-137	4
α-helix	138-140	3
α-helix	150-162	13
α-helix	173-189	17
α-helix	190-192	3
α-helix	196-200	5
β-strand	201-204	4	35
β-strand	207-215	9	34
β-strand	218-226	9	34
β-strand	229-232	4	35
α-helix	235-238	4
α-helix	242-247	6
β-strand	266-268	3	34
β-strand	276	1	34
β-strand	279	1	36
β-strand	287-294	8	35
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	35
β-strand	351-361	11	35
β-strand	372-381	10	35
β-strand	385-387	3	37
β-strand	402-404	3	37
α-helix	409-418	10

Chain 6: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	50	1	91
α-helix	55-66	12
α-helix	74-78	5
α-helix	100-113	14
α-helix	117-124	8
α-helix	132-141	10
α-helix	144-154	11
α-helix	157-161	5
β-strand	174-179	6	41
β-strand	183-187	5	41
β-strand	191-192	2	42
α-helix	201-202	2
β-strand	203-205	3	41
β-strand	214-220	7	42
β-strand	231-240	10	42
β-strand	249-252	4	42
α-helix	253-257	5
α-helix	259-260	2
β-strand	261	1	43
β-strand	266-275	10	42
α-helix	278-280	3
β-strand	297-298	2	42
α-helix	300-307	8
β-strand	311-321	11	42
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	43
α-helix	346-350	5
α-helix	353-355	3
α-helix	363-367	5

Chain 7: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21
β-strand	64-68	5	17
β-strand	78-82	5	17
α-helix	88-95	8
α-helix	98-101	4
β-strand	105-108	4	18
β-strand	111-113	3	18
α-helix	118-119	2
β-strand	124	1	17
β-strand	125-128	4	18
α-helix	136-155	20
β-strand	164-168	5	19
α-helix	174-176	3
β-strand	179-185	7	19
α-helix	187-191	5
α-helix	196-211	16
β-strand	215	1	20
β-strand	217-222	6	21
α-helix	223-229	7
α-helix	234-244	11
β-strand	251-256	6	21
β-strand	261-263	3	21
β-strand	271	1	20
α-helix	272-274	3
β-strand	275-285	11	19
β-strand	295-303	9	19
α-helix	310-319	10

Chain 8: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	90-91	2
α-helix	108-153	46
α-helix	163-165	3
α-helix	174-176	3
β-strand	177	1	22

45 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
39S ribosomal protein L32, mitochondrial	0	protein	188	Homo sapiens	Q9BYC8 (AlphaFold model)
39S ribosomal protein L33, mitochondrial	1	protein	65	Homo sapiens	O75394 (AlphaFold model)
39S ribosomal protein L34, mitochondrial	2	protein	92	Homo sapiens	Q9BQ48 (AlphaFold model)
39S ribosomal protein L35, mitochondrial	3	protein	188	Homo sapiens	Q9NZE8 (AlphaFold model)
39S ribosomal protein L39, mitochondrial	7	protein	338	Homo sapiens	Q9NYK5
39S ribosomal protein L40, mitochondrial	8	protein	206	Homo sapiens	Q9NQ50
39S ribosomal protein L4, mitochondrial	F	protein	311	Homo sapiens	Q9BYD3
39S ribosomal protein L9, mitochondrial	H	protein	267	Homo sapiens	Q9BYD2
39S ribosomal protein L11, mitochondrial	J	protein	192	Homo sapiens	Q9Y3B7
39S ribosomal protein L13, mitochondrial	K	protein	178	Homo sapiens	Q9BYD1
39S ribosomal protein L14, mitochondrial	L	protein	145	Homo sapiens	Q6P1L8
39S ribosomal protein L15, mitochondrial	M	protein	296	Homo sapiens	Q9P015

43 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8QU5_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (1), FASTA

>8QU5_2 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 3 (2), FASTA

>8QU5_3 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 4 (3), FASTA

>8QU5_4 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 5 (7), FASTA

>8QU5_5 39S ribosomal protein L39, mitochondrial (chains 7)
MEALAMGSRALRLWLVAPGGGIKWRFIATSSASQLSPTELTEMRNDLFNKEKARQLSLTP
RTEKIEVKHVGKTDPGTVFVMNKNISTPYSCAMHLSEWYCRKSILALVDGQPWDMYKPLT
KSCEIKFLTFKDCDPGEVNKAYWRSCAMMMGCVIERAFKDEYMVNLVRAPEVPVISGAFC
YDVVLDSKLDEWMPTKENLRSFTKDAHALIYKDLPFETLEVEAKVALEIFQHSKYKVDFI
EEKASQNPERIVKLHRIGDFIDVSEGPLIPRTSICFQYEVSAVHNLQPTQPSLIRRFQGV
SLPVHLRAHFTIWDKLLERSRKMVTEDQSKATEECTST

Sequence of entity 6 (8), FASTA

>8QU5_6 39S ribosomal protein L40, mitochondrial (chains 8)
MTASVLRSISLALRPTSGLLGTWQTQLRETHQRASLLSFWELIPMRSEPLRKKKKVDPKK
DQEAKERLKRKIRKLEKATQELIPIEDFITPLKFLDKARERPQVELTFEETERRALLLKK
WSLYKQQERKMERDTIRAMLEAQQEALEELQLESPKLHAEAIKRDPNLFPFEKEGPHYTP
PIPNYQPPEGRYNDITKVYTQVEFKR

Sequence of entity 7 (F), FASTA

>8QU5_7 39S ribosomal protein L4, mitochondrial (chains F)
MLQFVRAGARAWLRPTGSQGLSSLAEEAARATENPEQVASEGLPEPVLRKVELPVPTHRR
PVQAWVESLRGFEQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEV
RGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTV
KLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSVLLVDLTHEEMPQSIVEATSRLKTF
NLIPAVGLNVHSMLKHQTLVLTLPTVAFLEDKLLWQDSRYRPLYPFSLPYSDFPRPLPHA
TQGPAATPYHC

Sequence of entity 8 (H), FASTA

>8QU5_8 39S ribosomal protein L9, mitochondrial (chains H)
MAAPVVTAPGRALLRAGAGRLLRGGVQELLRPRHEGNAPDLACNFSLSQNRGTVIVERWW
KVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGR
NRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNV
KWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNF
EKPKTKRYKYWLAQQAAKAMAPTSPQI

Sequence of entity 9 (J), FASTA

>8QU5_9 39S ribosomal protein L11, mitochondrial (chains J)
MSKLGRAARGLRKPEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDI
KEGIPLPTKILVKPDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEI
ARIKAQDEAFALQDVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAIFLAAQKE
ADLAAQEEAAKK

Sequence of entity 10 (K), FASTA

>8QU5_10 39S ribosomal protein L13, mitochondrial (chains K)
MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM
NTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRT
MMERLHLFPDEYIPEDILKNLVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDYRL

Sequence of entity 11 (L), FASTA

>8QU5_11 39S ribosomal protein L14, mitochondrial (chains L)
MAFFTGLWGPFTCVSRVLSHHCFSTTGSLSAIQKMTRVRVVDNSALGNSPYHRAPRCIHV
YKKNGVGKVGDQILLAIKGQKKKALIVGHCMPGPRMTPRFDSNNVVLIEDNGNPVGTRIK
TPIPTSLRKREGEYSKVLAIAQNFV

Sequence of entity 12 (M), FASTA

>8QU5_12 39S ribosomal protein L15, mitochondrial (chains M)
MAGPLQGGGARALDLLRGLPRVSLANLKPNPGSKKPERRPRGRRRGRKCGRGHKGERQRG
TRPRLGFEGGQTPFYIRIPKYGFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPSQPIDLTQ
LVNGRGVTIQPLKRDYGVQLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYD
PRSLDIVCKPVPFFLRGQPIPKRMLPPEELVPYYTDAKNRGYLADPAKFPEARLELARKY
GYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMADKKILKPTDENLLKYYTS

Ligands and cofactors

ID	Name	Formula	Copies
PNS	4'-phosphopantetheine	C11 H23 N2 O7 P S	1
MG	Magnesium ion	Mg	48
ZN	Zinc ion	Zn	2

Primary citation

GTPBP8 plays a role in mitoribosome formation in human mitochondria. Cipullo, M., Valentin Gese, G., Gopalakrishna, S. et al. Nat Commun (2024) 15:5664-5664. DOI 10.1038/s41467-024-50011-x · PubMed

Other PDB entries of the same protein (UniProt Q9BYC8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OF0 2.2 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
7OF7 2.5 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7PO4 2.56 Å, Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded…
6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
7O9M 2.6 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
7OF6 2.6 Å, Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6…
9CN3 2.62 Å, Human 39S mitoribosome in complex with antibiotic Linezolid
7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…
9RU6 2.64 Å, Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P-…

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